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- PDB-5mgj: Crystal Structure of BAZ2A bromodomain in complex with 1-methylpy... -

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Basic information

Entry
Database: PDB / ID: 5mgj
TitleCrystal Structure of BAZ2A bromodomain in complex with 1-methylpyridine derivative 1
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7MX / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLolli, G. / Spiliotopoulos, D. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_169007 Switzerland
CitationJournal: Eur J Med Chem / Year: 2017
Title: Discovery of BAZ2A bromodomain ligands.
Authors: Spiliotopoulos, D. / Wamhoff, E.C. / Lolli, G. / Rademacher, C. / Caflisch, A.
History
DepositionNov 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / diffrn_radiation_wavelength / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5972
Polymers12,3811
Non-polymers2161
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.737, 95.737, 32.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / Tip5 / hWALp3


Mass: 12380.919 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1796-1898
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF9
#2: Chemical ChemComp-7MX / ethyl 4-chloranyl-1-methyl-6-oxidanylidene-pyridine-3-carboxylate


Mass: 215.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10ClNO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.08 % / Mosaicity: 0.56 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.87 Å / Num. obs: 10377 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.07 / Rrim(I) all: 0.218 / Net I/σ(I): 9.2 / Num. measured all: 100297
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.1610.11.0740.7851100
8.91-47.879.30.0580.998199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LZ2

4lz2


Resolution: 2.1→31.337 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.92
RfactorNum. reflection% reflection
Rfree0.2224 568 5.48 %
Rwork0.1919 --
obs0.1936 10359 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.36 Å2 / Biso mean: 35.9747 Å2 / Biso min: 11.33 Å2
Refinement stepCycle: final / Resolution: 2.1→31.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 14 124 991
Biso mean--29.27 39.27 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007895
X-RAY DIFFRACTIONf_angle_d1.0091207
X-RAY DIFFRACTIONf_chiral_restr0.035120
X-RAY DIFFRACTIONf_plane_restr0.006159
X-RAY DIFFRACTIONf_dihedral_angle_d13.959331
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1001-2.31140.32131350.250524202555
2.3114-2.64570.2251290.220324352564
2.6457-3.33270.23511400.199824452585
3.3327-31.34080.1931640.162224912655
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0119-0.00230.02580.00620.00540.0802-0.0319-0.03170.08080.0402-0.06910.0712-0.08060.0152-0.02110.194-0.1294-0.03390.22130.01320.281833.5012-20.518240.3088
20.0296-0.01040.00570.028-0.0090.0179-0.0052-0.0610.02910.0224-0.0463-0.0488-0.00220.0074-0.07790.095-0.1029-0.00760.3960.04630.184438.439-36.95429.5009
30.0012-0.0046-0.00250.1793-0.1110.13-0.08660.21170.1289-0.0194-0.03980.0854-0.07040.0618-0.18010.154-0.1558-0.03930.31110.09110.218129.8949-28.317228.3403
40.0104-0.01250.0190.0239-0.01410.24240.0139-0.03510.07060.03850.01910.0580.0390.0232-0.00270.0819-0.09060.010.2166-0.0280.141928.0545-34.951840.1774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1796 through 1810 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1811 through 1829 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1830 through 1872 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1873 through 1898 )A0

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